User: ompandey

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ompandey0
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Posts by ompandey

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Comment: C: How to do a confounding variable adjustment without using the treatment informat
... Thanks for your reply. Do you recommend to use output of vst(..,blind=TRUE) to be further used as an input to removeBatchEffect() for removing differences due to the confounders in the design? In the case of blind=FALSE, I am not sure about the impact of including/excluding treatment variable from ...
written 2.8 years ago by ompandey0
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Comment: C: How to use removeBatchEffect for removing effect of multiple confounding variabl
... Thanks Ryan for your quick reply. Your suggestions are really helpful. I am not sure, if I got you regarding exactly how to prevent removeBatchEffect() from changing the overall mean expression of each gene.  ...
written 2.8 years ago by ompandey0
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Comment: C: How to use removeBatchEffect for removing effect of multiple confounding variabl
... Thanks Aaron for your quick reply.  I have checked that at-least two of my confounders for being orthogonal to treatment effect or not. > tapply(as.numeric(covariates_df$TREAT),covariates_df$B, table) $`1` # male 1 2 # 1 as treated and 2 as untreated 32 29 $`2` # female 1 2 # 1 as treate ...
written 2.8 years ago by ompandey0
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How to use removeBatchEffect for removing effect of multiple confounding variables
... Hello Everyone, I am new to the limma based batch correction functionalities. I am trying to use removeBatchEffect() function from limma (3.24.6) package. I have three confounding variables, for which I want to remove their effect on the gene expression. While removing the effect of confounding var ...
limma deseq2 removebatcheffect written 2.8 years ago by ompandey0 • updated 2.8 years ago by Ryan C. Thompson7.2k
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How to do a confounding variable adjustment without using the treatment information?
... Hello Everyone, I am new to the DESeq2 based RNASeq analysis. I am using DESeq2 (version 1.8.1) with the objective of processing the RNASeq count data for further downstream analysis using Variance Stabilizing Transformation (VST) data. Using the adjusted and transformed RNASeq data, my aim is to d ...
deseq2 variancestabilizingtransformation rnaseq_analysis confounders written 2.8 years ago by ompandey0 • updated 2.8 years ago by Michael Love22k

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